Adaptive ensemble simulations of biomolecules

Peter M. Kasson, Shantenu Jha

Research output: Contribution to journalReview article

7 Citations (Scopus)

Abstract

Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of individual simulation trajectories and analyze statistics across them. Adaptive ensemble simulations offer a further level of sophistication and flexibility by enabling high-level algorithms to control simulations-based on intermediate results. We review some of the adaptive ensemble algorithms and software infrastructure currently in use and outline where the complexities of implementing adaptive simulation have limited algorithmic innovation to date. We describe an adaptive ensemble API to overcome some of these barriers and more flexibly and simply express adaptive simulation algorithms to help realize the power of this type of simulation.

Original languageEnglish (US)
Pages (from-to)87-94
Number of pages8
JournalCurrent Opinion in Structural Biology
Volume52
DOIs
StatePublished - Oct 2018

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All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

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Adaptive ensemble simulations of biomolecules. / Kasson, Peter M.; Jha, Shantenu.

In: Current Opinion in Structural Biology, Vol. 52, 10.2018, p. 87-94.

Research output: Contribution to journalReview article

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AB - Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of individual simulation trajectories and analyze statistics across them. Adaptive ensemble simulations offer a further level of sophistication and flexibility by enabling high-level algorithms to control simulations-based on intermediate results. We review some of the adaptive ensemble algorithms and software infrastructure currently in use and outline where the complexities of implementing adaptive simulation have limited algorithmic innovation to date. We describe an adaptive ensemble API to overcome some of these barriers and more flexibly and simply express adaptive simulation algorithms to help realize the power of this type of simulation.

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